Solvation, thermodynamics, and structure of biological
macromolecules
T-12 contributes to Los Alamos efforts in the molecular biophysics
and structural biology by developing and applying statistical
mechanical theories of hydration of biological macromolecules and
molecular assemblies in aqueous solution. These solvation phenomenon
are typically categorized as either hydrophobic or hydrophilic.
Hydrophobic effects are associated with solutes or solute fragments
that interact, generically, with water molecules through van der Waals
interactions. The noble gases and the simple alkanes, all sparingly
soluble in water, are examples of primitive hydrophobic solutes.
Hydrophilic solute interactions with water molecules typically include
either classic electrostatic or specific chemical interactions.
Examples are ammonia, formaldehyde, and peptides.
T-12 staff member Lawrence Pratt works on
these problems in collaboration with Gerhard Hummer and T-10 staff
member Angel García.
The viewgraphs (as pdf files) for some recent presentations follow.
This permits the audience access to the slides before the talk
and probably not all the slides would be shown.
Some research papers:
- L. R. Pratt and D. Chandler, J.
Chem. Phys. 67, 3683(1977): ``Theory of the hydrophobic
effect.''
- L. R. Pratt and D. Chandler, J. Chem. Phys. 73,
3434(1980): ``Effects of solute-solvent attractive forces on
hydrophobic correlations.''
-
L. R. Pratt and D. Chandler, J. Chem. Phys. 73, 3430(1980):
``Hydrophobic solvation of nonspherical solutes.''
- A. L. Nichols III and L. R. Pratt, J. Chem. Soc. Faraday
Symp. 17, 129(1982): ``Disentanglement of hydrophobic and
electrostatic contributions to the film pressures of ionic
surfactants.''
- B. Owenson and L. R. Pratt, J. Phys. Chem. 88,
2905(1984): ``Molecular statistical thermodynamics of model micellar
aggregates.''
- A. Pohorille, L. R. Pratt, S. K. Burt, and R. D. MacElroy, J.
Biomolec. Struct. Dyn. 1, 1257(1984): ``Solution influence
on biomolecular equilibria: Nucleic acid base associations.''
- L. R. Pratt, Ann. Rev. Phys. Chem. 36, 433(1985):
``Theory of hydrophobic effects.''
- L. R. Pratt and D. Chandler, Methods in Enzymology
127, 48(1985): ``Theoretical and computational studies of
hydrophobic interactions.''
- L. R. Pratt, B. Owenson, and Zhewei Sun, Advances in Colloid
and Interface Science 26, 69(1986): ``Molecular theory of
micelle formation in aqueous solution.''
- A. Pohorille and L. R. Pratt, J. Am. Chem. Soc.
112, 5066(1990): ``Cavities in molecular liquids and the theory
of hydrophobic solubilities.'' See also ``Simulated liquids point to
new solutions,'' Science News, 7 July 1990, page 5.
- L. R. Pratt, CLS Division 1991 Annual Review: ``Oil and
water don't mix.'' LA-UR-91-1783. National Technical Information
Service, U. S. Department of Commerce, 5285 Port Royal Rd.,
Springfield, VA 22161.
- L. R. Pratt and A. Pohorille, Proc. Nat. Acad. Sci. USA
89, 2995(1992): ``Theory of hydrophobicity: transient cavities
in molecular liquids.''
- L. R. Pratt and A. Pohorille, Proceedings of the EBSA
(Association of European Biophysical Societies) 1992 International
Workshop on Water-Biomolecule Interactions, edited by M. U. Palma,
M. B. Palma-Vittorelli, and F. Parak (Societa' Italiana de Fisica,
Bologna, 1993), pp. 261-268: ``Hydrophobic Effects from Cavity
Statistics.'''
- L. R. Pratt and R. A. Keller, J. Phys. Chem. 97,
10254 (1993): ``Estimate of the probability of diffusional misordering
in high-speed DNA sequencing.''
- L. R. Pratt, G. Hummer, and A. E. García, Biophys.
Chem. 51, 147(1994): `` Ion pair
potentials-of-mean-force in water .''
- G. Hummer, L. R. Pratt, and A. E. García, J. Phys.
Chem. 99, 14188(1995): `` The hydration free
energy of water .''
- G. Hummer, L. R. Pratt, and A. E. García, J. Phys.
Chem. 100, 1206(1996): `` Free energy of ionic
hydration .''
- G. Hummer, S. Garde, A. E. García, A. Pohorille, and L. R.
Pratt, Proc. Natl. Acad. USA 93, 8951 (1996): ``An
information theory model of hydrophobic interactions.'' See also the
commentary B. J. Berne, Proc. Natl. Acad. USA 93, 8800
(1996): ``Inferring the hydrophobic interaction from the properties of
neat water.''
- S. Garde, G. Hummer, A. E. García, M. E. Paulaitis, and L.
R. Pratt, Phys. Rev. Letts. 77, 4966 (1996): `` Origin of entropy
convergence in hydrophobic hydration and protein folding .''
- G. Hummer, L. R. Pratt, A. E. García, B. J. Berne, and S.
W. Rick, J. Phys. Chem. B 101, 3017 (1997), `` Electrostatic
potentials and free energies of polar and charged
molecules.''
- G. Hummer, L. R. Pratt, and A. E. García, J. Am. Chem.
Soc. 119, 8523 (1997), ``Multistate gaussian model for
polar and ionic hydration.''
- G. Hummer, L. R. Pratt, and A. E. García, J. Chem.
Phys. 107, 9275 (1997), `` Ion sizes and
finite-size corrections for ionic-solvation free energies.''
- L. R. Pratt, Hydrophobic Effects, in
The Encyclopedia
of Computational Chemistry,
Schleyer, P. v. R.; Allinger, N. L.;
Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.;
Schriener, P. R.; John Wiley & Sons, Chichester, 1998.
- G. Hummer, S. Garde, A. E. García, M. E. Paulaitis, and L.
R. Pratt, Proc. Natl. Acad. Sci USA 95, 1552 (1998):
``The pressure dependence of hydrophobic interactions is consistent
with the pressure denaturation of proteins.''
- L. R. Pratt and R. A. LaViolette, Molec. Phys.
94, 909(1998), ``
Quasi-chemical Theories of Associated Liquids.''
- G. Hummer, L. R. Pratt and A. E. García,
J. Phys. Chem. A 102, 7885(1998), `` Molecular theories and
simulation of ions and polar molecules in water.''
- L. R. Pratt, S. Garde, and G. Hummer, LA-UR-98-2712, proceedings
of the NATO Advanced Study Institute New Approaches to Old and New
Problems in Liquid State Theory: Inhomogeneous and Phase Separation in
Simple, Complex and Quantum Fluids: `` Theories of
Hydrophobic Effects and the Description of Free Volume in Complex
Liquids.''
- G. Hummer, S. Garde, A. E. García, M. E. Paulaitis, and
L. R. Pratt, J. Phys. Chem. B 102, 10469 (1998), ``Hydrophobic Effects on
a Molecular Scale.''
- S. Garde, A. E. García, L. R. Pratt, and G. Hummer:
Biophys. Chem. 78, 21(1999), ``Temperature Dependence of
the Solubility of Nonpolar Gases in Water.''
- M. A. Gomez, L. R. Pratt, G. Hummer, and S. Garde: J. Phys.
Chem. B 103, 3520(1999), ``Molecular Realism in
Default Models for Information Theories of Hydrophobic
Effects.''
- L. R. Pratt and S. B. Rempe, Simulation and Theory of
Electrostatic Interactions in Solution, AIP Conference Proceedings
492, (1999), eds. L. R. Pratt and G. Hummer, pp 172-201: ``Quasi-Chemical Theory
and Implicit Solvent Models for Simulations.''
- G. Hummer, L. R. Pratt, A. E. García, and M. Neumann,
Simulation and Theory of Electrostatic Interactions in
Solution, AIP Conference Proceedings 492, (1999), eds. L.
R. Pratt and G. Hummer, pp 84-103: ``Treatment of
Electrostatic Interactions in Computer Simulations and Calculation of
Thermodynamic Properties such as Free Energies and Pressures.''
- S. B. Rempe, L. R. Pratt, G. Hummer, J. D. Kress,
R. L. Martin, and A. Redondo, J. Am. Chem. Soc. 122,
966-967 (2000): ``The Hydration
of Li+ in Liquid Water.''
- S. B. Rempe, L. R. Pratt. G. Hummer, J. D. Kress, R. L. Martin,
and A. Redondo, J. Am. Chem. Soc. 122, 966-967 (2000):
``The Hydration of
Li+ in Liquid Water.''
- G. Hummer, S. Garde, A. E. García, and L. R. Pratt,
Chem. Phys. 258, 349-370(2000):
``New
Perspectives on Hydrophobic Effects.''
- S. B. Rempe and L. R. Pratt, LA-UR-00-2309: ``The Hydration of
Na+ in Liquid Water.''
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